Protein alpha-N-acetylation studied by N-terminomics

Cotranslational protein N-terminal modifications, including proteolytic maturation such as initiator methionine excision by methionine aminopeptidases and N-terminal blocking, occur universally. Protein alpha-N-acetylation, or the transfer of the acetyl moiety of acetyl-coenzyme A to nascent protein N-termini, catalysed by multisubunit N-terminal acetyltransferase complexes, generally takes place during protein translation. Nearly all protein modifications are known to influence different protein aspects such as folding, stability, activity and localization, and several studies have indicated similar functions for protein alpha-N-acetylation. However, until recently, protein alpha-N-acetylation remained poorly explored, mainly due to the absence of targeted proteomics technologies. The recent emergence of N-terminomics technologies that allow isolation of protein N-terminal peptides, together with proteogenomics efforts combining experimental and informational content have greatly boosted the field of alpha-N-acetylation. In this review, we report on such emerging technologies as well as on breakthroughs in our understanding of protein N-terminal biology.     

A Saccharomyces cerevisiae Model Reveals In Vivo Functional Impairment of the Ogden Syndrome N-Terminal Acetyltransferase NAA10 Ser37Pro Mutant

N-terminal acetylation (Nt-acetylation) occurs on the majority of eukaryotic proteins and is catalyzed by N-terminal acetyltransferases (NATs). Nt-acetylation is increasingly recognized as a vital modification with functional implications ranging from protein degradation to protein localization. Although early genetic studies in yeast demonstrated that NAT-deletion strains displayed a variety of phenotypes, only recently, the first human genetic disorder caused by a mutation in a NAT gene was reported; boys diagnosed with the X-linked Ogden syndrome harbor a p.Ser37Pro (S37P) mutation in the gene encoding Naa10, the catalytic subunit of the NatA complex, and suffer from global developmental delays and lethality during infancy. Here, we describe a Saccharomyces cerevisiae model developed by introducing the human wild-type or mutant NatA complex into yeast lacking NatA (NatA-Δ). The wild-type human NatA complex phenotypically complemented the NatA-Δ strain, whereas only a partial rescue was observed for the Ogden mutant NatA complex suggesting that hNaa10 S37P is only partially functional in vivo. Immunoprecipitation experiments revealed a reduced subunit complexation for the mutant hNatA S37P next to a reduced in vitro catalytic activity. We performed quantitative Nt-acetylome analyses on a control yeast strain (yNatA), a yeast NatA deletion strain (yNatA-Δ), a yeast NatA deletion strain expressing wild-type human NatA (hNatA), and a yeast NatA deletion strain expressing mutant human NatA (hNatA S37P). Interestingly, a generally reduced degree of Nt-acetylation was observed among a large group of NatA substrates in the yeast expressing mutant hNatA as compared with yeast expressing wild-type hNatA. Combined, these data provide strong support for the functional impairment of hNaa10 S37P in vivo and suggest that reduced Nt-acetylation of one or more target substrates contributes to the pathogenesis of the Ogden syndrome. Comparative analysis between human and yeast NatA also provided new insights into the co-evolution of the NatA complexes and their substrates. For instance, (Met-)Ala- N termini are more prevalent in the human proteome as compared with the yeast proteome, and hNatA displays a preference toward these N termini as compared with yNatA.Up to 85% of soluble eukaryotic proteins carry an N-terminal acetyl group at their N terminus, which is the result of a co-translational protein modification referred to as N-terminal protein acetylation (Nt-acetylation) or N^α-acetylation (1). This presumed irreversible protein modification is catalyzed by a specific category of the GCN5-related N-acetyltransferase domain containing superfamily of acetyltransferases; the ribosome associated N-terminal acetyltransferases or NATs¹ (2). NATs catalyze the acetyl transfer from acetyl coenzyme A (Ac-CoA) to a primary α-amine of the first amino acid residue of a nascent protein chain. In eukaryotes, NATs are composed of at least one catalytic subunit and mainly target different substrate N termini based on their N-terminal sequences (3).To date, five human NATs hNatA, hNatB, and hNatC; constituting the major human NAT complexes, and hNatD and hNatF have been identified and their substrate specificity characterized (1, 4–8). In addition, a putative hNatE complex has been described (9–10). Except for NatF, which is only expressed in higher eukaryotes (1), the substrate specificity profiles of the NatA-E complexes seem to be conserved among eukaryotes (5–9, 11–13).Contrary to the original assumption that Nt-acetylation protected proteins from degradation (14), it was more recently demonstrated that this modification creates specific degradation signals (termed Ac/N-degrons) in cellular proteins, thereby diversifying this original view substantially. These degrons target at least some Nt-acetylated proteins for the conditional degradation by a novel branch of the N-end rule pathway, an ubiquitin-dependent proteolytic system (15–16). In addition, numerous reports implicate Nt-acetylation in cellular differentiation, survival, metabolism, and proliferation, thereby linking it to cancer (17–18). As such, Nt-acetylation is now linked to a whole range of molecular implications including protein destabilization and degradation by the Nt-acetylation dependent recruitment of ubiquitin ligases (15–16), protein translocation (19), membrane attachment (20), and protein complex formation (21).Among all characterized NATs, NatA displays the broadest substrate specificity profile and thus represents the primary NAT in terms of substrate N termini as it is responsible for the Nt-acetylation of the methionine aminopeptidase (MetAP) iMet-processed serine, threonine, alanine, glycine, and valine starting N termini (3). The human NatA complex is composed of two essential subunits; the catalytic subunit hNaa10 (hARD1) and the regulatory subunit hNaa15 (NATH/hNAT1) (4). Deregulations of hNaa10 and/or NatA expression have been linked to various signaling molecules including hypoxia inducible factor-1α, DNA methyltransferase1/E-cadherin, β-catenin/cyclin D1, and Bcl-xL, showing its involvement in hypoxia, tumorigenesis, cell cycle progression, and apoptosis (17, 22–26).Recently, the first structures of NATs and a NAT-complex were solved, providing a molecular understanding of the sequence specific Nt-acetylation of protein N termini (27–30). Structural analyses of noncomplexed Naa10 and NatA from Schizosaccharomyces pombe reveal an allosteric modulator function of Naa15 in steering Naa10 specificity and provide a rational for the distinctive substrate specificity profiles observed when assaying non-complexed versus complexed Naa10 (10, 27), with both forms co-existing in cells (10). In particular, three essential catalytic Naa10 residues were found to be incorrectly positioned in non-complexed Naa10, while these shift into the active site in Naa15-complexed Naa10, thereby permitting canonical NatA-mediated Nt-acetylation. Interestingly, noncomplexed Naa10 was shown to efficiently Nt-acetylate glutamate and aspartate starting N termini, whereas poorly acetylating canonical NatA type N termini (10). The study of Liszczak et al. further showed that NatA substrate binding specificity was coupled to the catalytic mechanism being used (27). More specifically, an essential glutamate residue (Glu24 in the protein accession {"type":"entrez-protein","attrs":{"text":"Q9UTI3","term_id":"74625957","term_text":"Q9UTI3"}}Q9UTI3 (Swiss-Prot)) involved in catalysis, precludes methionine from entering the specificity pocket, whereas cognate NatA substrate N-terminal residues can easily be accommodated. Interestingly, and in contrast to NatA, both wild-type Naa10 and Glu24 mutated Naa10 (Naa10 E24A) were still capable of Nt-acetylating acidic amino acid starting N termini, most likely because of the substrate side-chain carboxyl moiety acting as a functional replacement group in the process of catalysis, whereas essentially no activity could be observed when probing a cognate NatA substrate (27).Early yeast studies demonstrated that strains with mutated or deleted NAT genes were viable, but displayed a number of different phenotypes (31). For NatA, the first phenotypes described were defects in sporulation, mating, and entry into stationary phase when NAA10 (ARD1) was mutated (32). Four years later, the overlapping phenotypes of NAA10 and NAA15 (NAT1) mutant strains, revealed, along with other data, that Naa10 and Naa15 are in fact components of the NatA acetyltransferase complex (33–34). As compared with NatA phenotypes, NatB phenotypes are more severe, including slow growth and defects in mitochondrial inheritance (35–36). NatC subunits were initially found to be essential for propagation of the l-A dsRNA virus, and further for growth on nonfermentable carbon sources (37–39). The first reports implicating NAT gene point mutations in human genetic disorders only recently emerged. More specifically, two different point mutations in the X-linked NAA10 gene were both found to cause developmental delays and were linked to the Ogden syndrome (S37P) (40) and intellectual disability (R116W) (41), highlighting the essential importance of NATs and protein Nt-acetylation in biology and disease. Further, in Caenorhabditis elegans (42), Drosophila melanogaster (43), and Trypanosoma brucei (44), Naa10 was proven to be essential and, strengthened by the observed detrimental effects of NAA10 mutations (40–41), the NAA10 gene function is also believed to be essential in human.Ogden syndrome boys harboring the p.Ser37Pro variant in the gene encoding Naa10 are characterized by craniofacial abnormalities, failure to thrive, developmental delay, hypotonia, cardiac arrhythmias, cryptorchidism, and an aged appearance, ultimately resulting in mortality during infancy (40). Although this mutation was shown to significantly impair Naa10 catalytic activity in vitro, we here assessed the influence and functional in vitro and in vivo consequences of this mutation on NatA complex formation and NatA activity in a yeast model. By phenotypic screening in yeast, we show that hNaa10 S37P displays a significantly impaired functionality in vivo. Further, using immunoprecipitation, we show that the human Naa10-Naa15 complex formation is negatively affected by the S37P mutation, and that immunoprecipitated hNatA S37P also displays a reduced in vitro catalytic activity as compared with wild-type hNatA. Finally, quantitative Nt-acetylome analyses suggest that reduced Nt-acetylation of one or more target substrates contributes to the pathogenesis of the Ogden syndrome.     

The MMP-9 -1562 C/T Polymorphism in the Presence of Metabolic Syndrome Increases the Risk of Clinical Events in Patients with Coronary Artery Disease

Background and Objectives

Elevated levels of matrix metalloproteinase (MMP)-9 have been associated with the metabolic syndrome (MetS) and cardiovascular events. The MMP-9 −1562 C/T polymorphism has furthermore been shown as a risk factor for coronary artery disease (CAD). The non-favourable cardiometabolic state in MetS may increase the risk. We aimed to investigate the influence of MMP-9 −1562 C/T polymorphism in subjects with CAD and MetS.

Methods

Patients (n = 1000) with verified CAD stratified in Mets +/− (n = 244/756), were analyzed for the MMP-9 −1562 C/T polymorphism and related to clinical events after 2 years follow-up. Serum levels of total MMP-9 and tissue inhibitor of matrix metalloproteinases (TIMP)-1were analyzed in all, whereas MMP-9 activity, extracellular matrix metalloproteinase inducer (EMMPRIN), and expression of the two genes were analyzed in a subset of 240 randomly selected patients.

Results

Totally, 106 clinical endpoints were recorded. In MetS; the T-allele associated with 5.5 fold increase in event rate (p<0.0001), increased with number of MetS components, a 117% increase in total MMP-9 levels (TT homozygous, p = 0.05), significantly higher total- and endogenous active MMP-9 and TIMP-1 levels (p<0.01 all), and EMMPRIN was inversely correlated with pro- and endogenous active MMP-9 (p<0.05, both). In non-MetS; the T-allele was not associated with new events, nor higher MMP-9 levels. EMMPRIN was significantly correlated with total MMP-9 and TIMP-1 (p<0.01, both) and the two genes were inter-correlated (p<0.001).

Conclusion

In CAD patients with MetS, the MMP-9 T-allele increased the risk of clinical events, probably mediated through elevated MMP-9 levels and altered MMP-9 regulation.     

A new automated method for isolation of Chlamydia trachomatis from urine eliminates inhibition and increases robustness for NAAT systems

Chlamydia trachomatis is a leading cause of sexually transmitted infection. Diagnostic methods with easy non-invasive sample collection are important to increase testing and hence to reduce the spread of this infection. To enable more use of urine samples in C. trachomatis diagnostics, automation is an absolute requirement since obtaining high-quality DNA from urine specimens involves extensive processing.

Here, we present a study in which a new automated sample preparation method, BUGS'n BEADS™ STI (BnB STI), was used up-front of the BDProbeTec™ ET end point analysis and compared with the full BDProbeTec™ ET method to analyze C. trachomatis in 1002 urine samples.

The BnB STI system represents a new concept within magnetic sample preparation in which bacteria are first isolated from the sample material followed by purification of bacterial nucleic acid using the same magnetic particles. Similar sensitivity and specificity were obtained with both methods. None of the samples processed with BnB STI inhibited the BDProbeTec™ ET test whereas 1.8% showed inhibition when processed according to the manual BDProbeTec™ ET DNA preparation method. Moreover, the average MOTA scores obtained with the BnB STI system were 48% higher for all amplification controls and 57% higher for positive samples, compared to the manual sample preparation. Based on these results and the significant reduction in hands-on-time for urine sample processing, the automated BnB STI sample preparation method was implemented for routine analysis of C. trachomatis from urine samples.     

Classification and phylogeny for the annotation of novel eukaryotic GNAT acetyltransferases

The enzymes of the GCN5-related N-acetyltransferase (GNAT) superfamily count more than 870 000 members through all kingdoms of life and share the same structural fold. GNAT enzymes transfer an acyl moiety from acyl coenzyme A to a wide range of substrates including aminoglycosides, serotonin, glucosamine-6-phosphate, protein N-termini and lysine residues of histones and other proteins. The GNAT subtype of protein N-terminal acetyltransferases (NATs) alone targets a majority of all eukaryotic proteins stressing the omnipresence of the GNAT enzymes. Despite the highly conserved GNAT fold, sequence similarity is quite low between members of this superfamily even when substrates are similar. Furthermore, this superfamily is phylogenetically not well characterized. Thus functional annotation based on sequence similarity is unreliable and strongly hampered for thousands of GNAT members that remain biochemically uncharacterized. Here we used sequence similarity networks to map the sequence space and propose a new classification for eukaryotic GNAT acetyltransferases. Using the new classification, we built a phylogenetic tree, representing the entire GNAT acetyltransferase superfamily. Our results show that protein NATs have evolved more than once on the GNAT acetylation scaffold. We use our classification to predict the function of uncharacterized sequences and verify by in vitro protein assays that two fungal genes encode NAT enzymes targeting specific protein N-terminal sequences, showing that even slight changes on the GNAT fold can lead to change in substrate specificity. In addition to providing a new map of the relationship between eukaryotic acetyltransferases the classification proposed constitutes a tool to improve functional annotation of GNAT acetyltransferases.     

Resource partitioning among cape foxes,bat-eared foxes,and black-backed jackals in South Africa

Cape foxes (Vulpes chama) and bat-eared foxes (Otocyon megalotis) are sympatric with black-backed jackals (Canis mesomelas) over much of southern Africa, although competition with and/or predation by jackals may suppress local populations of both fox species. From 2005 to 2008, we captured, radio-collared, and monitored 11 cape foxes, 22 bat-eared foxes, and 15 black-backed jackals on a game ranch in South Africa to investigate their spatial, habitat, temporal, and dietary resource overlap. Mean annual home-range sizes were 27.7 km² for cape foxes, 5.0 km² for bat-eared foxes, and 17.8 km² for jackal family groups. Home ranges overlapped completely between species, although core areas overlapped less (<45%), with cape foxes and jackals overlapping the least (12%). When active, cape foxes, but not bat-eared foxes, used core areas of jackal groups less than expected. Additionally, both fox species used jackal core areas less than expected for their den sites, suggesting areas outside jackal core areas were used as refuges by foxes. Strong levels of habitat partitioning were not apparent at the study site or home-range levels, although habitat selection for den sites differed between jackals and cape foxes. Jackals were the most diurnal across seasons, whereas cape foxes were the most nocturnal. Diets overlapped little (R₀ = 0.20–0.34) among the canid species, with bat-eared foxes overlapping the least with the others. Jackals killed at least 5 collared bat-eared foxes and 1 collared cape fox, indicating potential interference competition, probably for exclusive use of territorial space rather than over shared resources. We conclude that bat-eared foxes coexisted with jackals primarily by their dietary specialization and group living. Cape foxes coexisted with jackals by exhibiting high levels of spatial, habitat, temporal, and dietary partitioning. Surprisingly, the fox species exhibited positive associations with each other. Our results show the mechanisms that may allow jackals to suppress fox populations, yet also show how foxes, in turn, use different mechanisms to coexist with a dominant canid. © 2012 The Wildlife Society.